Virioplankton shotgun metagenome from Chesapeake Bay water sample collected at the Smithsonian Environmental Research Center in Edgewater, Maryland. The sample was deeply sequenced using 77 million paired-end 150 bp Illumina reads and 350,000 long single-molecule PacBio reads averaging 1,700 bp in length. Objectives of the study were to evaluate the utility of single-molecule real time (SMRT) PacBio sequencing for metagenomics and to deeply sample virioplankton diversity. Hybrid assembly of short (Illumina) and long (PacBio) read sequence data showed substantial improvements in the yield of genome-length high quality contigs from the viral metagenome. Specifically, the assembly yielded 1,079 contigs greater than 20 kb, 62 of which were circular and likely complete dsDNA viral genomes. Phylogenetic analysis of the long viral contigs provided a high-resolution view of previously unknown viral diversity that was unattainable through either technology alone. Additionally, sequencing of marker gene PCR amplicons (using PacBio SMRT circular consensus protocol) was utilized to examine the depth of shotgun metagenome sampling.